This is an easy fix. The spirit of the rule is to protect the worst 10 teams picks.
Make an exception this year so the the Mets 11 overall pick is protected and going forward if any teams can't sign their top 10 protected pick as punishment have them pick 11. This allows them to still have a high pick the next year but punishes them in a way by that pick not being protected. Its a really east fix and hopefully Selig does the right thing.